Download Commensal Flora May Play Key Role in Spreading Antibiotic

Commensal Flora May Play Key Role in
Spreading Antibiotic Resistance
We need to learn more about commensal flora if we are to better
manage this particular window of vulnerability to antibiotic resistance
Antoine Andremont
particular window of vulnerability to antibiotic
ntibiotic resistance among commensal bacteria represents a major averesistance.
nue for the development of resistance in bacterial pathogens.
Assessing How Commensal Flora
Although the concept that commenContribute to Resistance Remains Difficult
sal flora play a major role in disseminating bacterial resistance was developed at least 30 years
Assessing the role of commensal flora in the
ago, it was set aside for several reasons.
development of antibiotic resistance among
First, the more immediate threat to humans
pathogens is difficult because, typically, resisfrom resistant bacteria is due to
tance increases first in the compathogens, not commensals. Secmensal flora but is transferred to
ond, it is much easier to study simpathogens only afterwards. Thus,
Assessing the
pler mechanisms of resistance in sinpatients who become infected with
role of
gle species than to follow gene
resistant bacteria usually are not
commensal
transfers among unrelated species
those in whom the selecting antibiflora in the
within complex ecosystems. Third,
otics were first used.
resistance was not considered a maFor instance, the rise in quinodevelopment of
jor public health problem when new
lone
resistance of pneumococci in
antibiotic
antibiotics were being made availCanada
occurred five years after
resistance
able on a regular basis—masking
these antibiotics came into use,
among
the growing magnitude of this probeven though they were used for
pathogens
is
lem and postponing the onset of antreating respiratory tract infecdifficult
tibiotic failures in clinical settings.
tions, according to Danny K. Chen
Strategies for involving comand coworkers from the University
because,
mensal bacteria to reduce antibiof Toronto. Also, trimethoprimtypically,
resistant respiratory tract bacterial
otic resistance in clinical practice
resistance
pathogens were detected in a San
cover only a very small number of
increases first
Francisco hospital following a rise
situations, meaning that reduced
in the
in usage of this drug to prevent
antibiotic use remains the major
commensal
parasitic Pneumocystis carinii inmeans for controlling resistance.
flora
fections in AIDS patients (Fig. 1),
Even if national and international
according to Jeffrey N. Martin and
agencies succeed in curbing uncolleagues from the University of
warranted uses of antibiotics,
California, San Francisco.
however, there always will be clinical conditions
in which antibiotic treatments are necessary.
In both these instances, resistance was likely
selected in commensal flora and later transferred
Hence, we will need to learn more about the
to pathogens. Indeed, there are two major aveimpact of antibiotic treatments on resistance in
nues for the emergence and spread of antibiotic
commensal flora if we are to better manage this
A
Antoine Andremont
is Professor of microbiology at Xavier
Bichat Medical
School, University
of Paris 7 (Paris,
France). He heads
the Bacteriology
Laboratory, Groupe
Hospitalier Bichat
Claude Bernard,
Paris, France.
Volume 69, Number 12, 2003 / ASM News Y 601
pigs are more frequently colonized by drugresistant commensal bacteria than are those
of nonfarmers with whom they are closely
matched.
Patients in hospitals are more likely to be
colonized by resistant bacteria than are individuals who have not been hospitalized.
Moreover, hospital workers have a high
rate of carriage of drug-resistant bacteria,
according to several studies. However, these
studies have tended to explore how resistant
bacteria are transmitted, rather than to
quantify the risk of increased prevalence of
resistant commensal flora among health
care personnel in contact with hospitalized
patients.
FIGURE 1
Commensals Could Be Highly Efficient
Contributors to Resistance
An example of the indirect impact of antibiotics on bacterial resistance. The graph
shows the increase in prevalence of pneumococci with reduced susceptibility to
fluoroquinolones (bars) following the increase in fluroquinolone usage (line). (see
Chen et al., N. Engl. J. Med. 341:233–239, 1999).
resistance in pathogenic bacteria, the first being
by direct selection of resistant mutants within
the population of pathogenic bacteria at the site
of infection. The second is indirect, involving
initial selection of resistant bacteria among commensal flora, followed by horizontal transfer of
resistance genes to pathogenic species.
Transfer of resistance genes from commensal
to pathogenic bacteria was described as early as
1959 by Japanese researchers, who were studying Escherichia coli, a commensal found in the
colon of humans, and Shigella dysenteriae, a
pathogen responsible for causing diarrhea that
is particularly deadly in developing countries.
More recently, investigators identify several
settings as likely sources of antibiotic resistance
traits found in intestinal enterobacteria occupying the human gastrointestinal (GI) tract. For
instance, close contact between humans and
farm animals, particularly those raised in large
production facilities, is associated with an increased prevalence of resistance to such drugs.
For instance, we recently showed that not only
the intestinal ecosystem, but also the nasal and
pharyngeal ecosystems among farmers raising
602 Y ASM News / Volume 69, Number 12, 2003
The indirect mechanism for generating bacterial resistance in pathogens is more efficient than direct selection for several reasons. First, among commensal flora, there
are many more targets than within an
infectious site in terms of numbers of species—
several hundreds versus a single species of
pathogen—and in terms of numbers of bacterial
cells, around 1014 commensals versus 108 –9 cells
of a particular pathogen.
Second, because the commensal genetic pool
is so large, it encompasses many more potential
means for conferring resistance, including not
only single-nucleotide mutations but also complex resistance mechanisms that ordinarily remain more or less silent within subdominant
species.
Third, resistant commensal flora may be selected each time an antibiotic is administered,
irrespective of the health status of the host,
whereas resistant pathogens are subject to selective pressure only when particular patients actually are infected with those bacteria. This point
is important because so many patients who receive antibiotics are not actually infected by
pathogens but, instead, are being treated prophylactically, or the cause of the infection is a
virus that is not susceptible to the drug being
administered. In animals, the proportion of noninfected recipients of antibiotic agents is even
greater than among humans.
In addition, pharmacodynamics and pharmacokinetics of antibiotics may favor the selection
of resistance amid commensal flora rather
FIGURE 2
than among pathogens. Indeed, we know
that low antibiotic doses and prolonged
treatments favor the emergence of resistance. Hence, antibiotic regimens take this
possibility into account and thus are set to
deliver appropriate concentrations of drug
to a particular site of infection.
However, these regimens typically do
not take into account what happens at
various surfaces where commensals may
encounter those drugs. For instance, after
patients are administered typical doses of
the antibiotic ciprofloxacin, its concentrations vary from 2 to 5 mg/liter in the sweat
of those patients, according to Niels
Hoı̈by and colleagues at the University of
Copenhagen in Denmark. Similarly, this
drug ranges from 3 to 5 mg/liter in feces,
according to Sophie Pecquet and other
colleagues in my laboratory, but only 0.5
to 1.5 mg/liter in the saliva and 0.3 to 0.5
mg/liter in nasal secretions as reported by
Rabih Darouiche and colleagues at the
Veterans Administration Medical Center
(VAMC) in Houston, Tex.
Role of anaerobes in colonization resistance in humans. During treatment with
There are three major bacterial ecosystems
regimens of antibiotics with activity against anaerobic organisms (black bars) the
in humans, including the intestinal, the cutafecal concentrations of vancomycin-resistant enterococci (VRE) increased in most
neous ones, and that of the upper respiratory
patients whereas it was stable or slightly decreased in those with regimens of
antibiotics with minimal activity against anaerobes (grey bars) (see Donskey et al.)
tract. Variations in drug concentration are a
source of differential selective pressures on
these commensal ecosystems, thus explaining
cess appears to involve anaerobic flora exerting
why resistance occurs so commonly after antibicolonization resistance in humans, according to
otic treatments. Each of these commensal ecosysCurtiss J. Donskey and colleagues at the VAMC
tems is affected to some extent during antibiotic
in Cleveland, Ohio. They showed that fecal
treatments.
counts of enterococci that are resistant to glycopeptide antibiotics increase significantly among
Commensals in the Intestinal System
patients who were treated with antibiotics that
Provide Insights about Drug Resistance
are active against anaerobic microorganisms
The intestinal commensal ecosystem is by far the
compared to those of patients who were treated
best studied and also the most populous, conwith other antibiotics having minimal activity
taining 1014 colony forming units (CFU) from
against anaerobes (Fig. 2).
several hundred species. For many decades, exColonization resistance also prevents the inperts said that the intestinal flora is very stable
testinal ecosystem from being colonized by exwithin each individual and among individuals of
ogenous bacteria, thus stabilizing the intestinalthe same species. The anaerobes at around 1011–
flora against newcomers. However, although a
1012 CFU/g of intestinal content dominate this
dominant lactobacillus strain can be very stable
ecosystem, in which enterobacteria and enteroin some subjects, it can vary greatly in others,
cocci are relatively minor players ranging from
according to Anne L. McCartney and colleagues
106–108 CFU/g.
from the University of Otago in New Zealand.
What distinguishes these two types of individuHow these population balances are mainals remains to be investigated.
tained is poorly understood, although the pro-
Volume 69, Number 12, 2003 / ASM News Y 603
FIGURE 3
Antibiotics promote colonization by resistant bacteria. In gnotobiotic mice harboring
microflora, a susceptible strain of E. coli (open squares) within a complex human,
multiresistant strains of Serratia liquefaciens (open circles) are rapidly eliminated
just as resistant E. coli transconjugant (black squares). During treatment with
ampicillin both resistant strains are eliminated while the susceptible E. coli disappeared (downward arrows indicate the lower limit of detection of a given strains)
(see Duval-Iflah et al., Infect. Immun. 28:981–990).
Colonization resistance has been extensively
studied in gnotobiotic mice that are inoculated
with human fecal flora, providing a relatively
convenient means for mimicking and thus investigating relationships among intestinal flora that
are typical of humans. For instance, Yvonne
Duval-Iflah, Cyrille Tancrède, and colleagues
from Institut National de la Recherche
Agronomique in Jouy-en-Josas, France, studied
a multiantibiotic-resistant strain of Serratia, an
enterobacterial species that does not belong to
the commensal flora of humans. In the basal
state before being treated with antibiotics, this
species was rapidly eliminated from such mice
even after repeated inoculations (Fig. 3). Even
so, these transient enterobacteria can transfer
their drug resistance gene-carrying plasmids to
E. coli that are residents of the GI tract, although the resulting transconjugants are also
rapidly eliminated.
However, when such mice are being actively
treated with antibiotics, the resistant strains rapidly establish residence in the GI tract, while
drug-susceptible strains disappear. Also of note,
604 Y ASM News / Volume 69, Number 12, 2003
the counts of drug-resistant enterobacteria
are higher than those of susceptible E. coli
before treatment. After antibiotic treatments cease, total counts of enterobacteria
return to baseline levels, suggesting colonization resistance is restored. Moreover, the
multiresistant strain of Serratia is eliminated but the remaining and predominant
E. coli population consists of transconjugants.
Altogether, this study suggests that inoculating exogenous resistant bacteria while
administering antibiotics could lead to prolonged modifications in bacterial resistance
within intestinal commensal bacteria. Such
a sequence of events probably also can occur among humans. Moreover, even in developed countries, industrialized foods can
be a source of drug-resistant gram-negative
and gram-positive bacteria. Maintaining a
sterile diet strongly reduces intestinal colonization by drug-resistant bacteria.
Antibiotic treatments can significantly affect the prevalence of bacterial resistance
among intestinal enterobacteria. For instance, within two weeks of taking trimethoprim, drug-resistant strains take over
the enterobacterial intestinal population in
subjects taking this drug, and this effect
lasts several weeks after drug treatment ends.
Colonization by enterobacteria resistant to the
antibiotic being administered seems to increase
linearly with the extent of treatment. The prevalence of carriage of resistant E. coli varies from
one country to another, with resistance often
more pronounced in developing than in developed countries, most probably because of the
wider availability of drugs without prescription
among the former.
Resistant commensal enterobacteria can circulate between individuals. Travelers to developing countries may be colonized by resistant
enterobacteria in the absence of antibiotic treatment. Even in developed countries with high
hygienic standards, resistant enterobacteria bacteria may disseminate within households. Several additional factors appear to influence the
extent of colonization by antibiotic-resistance
enterobacteria. For instance, drug-resistant bacteria colonizing Nepalese people decrease with
population density, access to allopathic medical
care, and distance from the capital of the country, according to Judd L. Walson and colleagues
from Tufts University Medical School in
Boston, Mass.
In general, there is little doubt that intestinal enterobacteria constitute a pool of antibiotic-resistant microorganisms. Moreover, there is evidence pointing to a
correlation between the resistance among
commensal enterobacteria and that found
among enterobacterial pathogens, not only
at the individual level but also at the population level in a given country.
FIGURE 4
Dissemination of Resistance within
Human Ecosystems
Antibiotic resistance genes spread among
enterobacteria in the GI tracts of humans as
well as several other animal species. Resistance genes, such as tetQ that confers resistance to tetracycline and erm that confers
resistance to erythromycin, can exchange
among Bacteroides spp. and among Bacteroides and other anaerobic genera that populate the human colon in high densities.
These genes are homologous to those that confer
resistance to these antibiotics in enterobacteria,
suggesting that multiple exchanges can occur
among enterobacteria and anaerobes.
Gene exchanges probably also occur in other
human ecosystems, particularly in the oropharynx between Streptococcus pneumoniae and
other non-groupable streptococci. For instance,
S. pneumoniae become resistant to penicillin
after genes encoding similar penicillin-binding
proteins (PBPs), which serve as target proteins of
␤-lactam antibiotics, recombine to form mosaic
PBPs. Often, parts of those recombined genes
derive from non-groupable streptococci, which
tend to be more resistant to antibiotics.
Moreover, genes encoding quinolone resistance
can be transformed and expressed in S. pneumoniae, with the rate being higher when donor
species are phylogenetically close to S. pneumoniae, according to Laurent Gutmann and his
group at the University of Paris VI in France. These
investigators showed that carriage of quinoloneresistant non-groupable streptococci is just as frequent in hospitalized patients that received quinolone as in those that had not, but this rate is much
higher than in individuals who had not been hospitalized. This finding suggests that there is a high
rate of antibiotic resistance gene transfer and dis-
Correlation between resistance to beta-lactam in S. pneumoniae and beta-lactam
use in various European countries; DDD are defined daily doses, and R is the rate
of strains with decreased susceptibility to penicillin (see http://www.earss.rium.nl).
semination within the pharyngeal flora of hospitalized patients.
Antibiotic resistance among staphylococci is a
major public health problem in hospitals worldwide. Excretion of antibiotics, such as ciprofloxacin in sweat during treatments, is associated with increased skin colonization by
ciprofloxacin-resistant S. epidermidis. Also, it is
assumed that the mecA gene that confers resistance to all ␤-lactams in S. aureus originates in
coagulase-negative staphylococci. For example,
in S. sciuri, a widely distributed coagulase-negative species, even though the mecA gene is
present, resistance is expressed only in mutants
that are derepressed for expression of the effector PBP2a protein, according to Shang Wei Wu
and colleagues from the Rockefeller University
in New York, N.Y. Furthermore, resistance can
transfer from derepressed S. sciuri to S. aureus.
Means for Reducing Antibiotic Resistance
Include Role for Commensal Flora
Reducing antibiotic use seems to be the best
means for reducing overall resistance. For short-
Volume 69, Number 12, 2003 / ASM News Y 605
FIGURE 5
Relationship between antibiotic use and decrease of resistance rates in the
community. The progressive discontinuation of avoparcin (AVO) usage was followed by a progressive reduction in the fecal rate of colonization by glycopeptide
resistant enterococci in community-living subjects from Saxony-Anhalt state in
Germany (see Klare et al., Microb. Drug Resist. 5:45–52). (AVO was a glycopeptide
heavily used in Europe as growth promoter in animal husbandry).
term studies, such as those performed in hospital
settings, the temporal relationship between antibiotic use and resistance may appear complex,
perhaps requiring sophisticated statistical analysis to account for delays between changes in
antibiotic use and in resistance rates, according
to Dominique Monnet from the Staten Serum
Institute in Copenhagen.
Nonetheless, some examples are being documented for pathogenic strains, particularly S.
pneumoniae. In Iceland, for instance, reducing
antibiotic use by 13% led to an estimated 10%
decrease in resistance to penicillin in that species, according to Daren J. Austin and colleagues
from the University of Oxford in England. Similarly in France, decreased antibiotic resistance
of S. pneumoniae followed reductions in antibiotic use in a population-based intervention, according to Didier Guillemot from the Pasteur
Institute in Paris.
More generally in Europe, this relationship
between reduced antibiotic use in a particular
population segment and lowered levels of antibiotic resistance among pathogenic species circulating within that population is well demon-
606 Y ASM News / Volume 69, Number 12, 2003
strated—for instance, consider a countryby-country comparison of susceptibility-topenicillin rates among S. pneumoniae
isolates (Fig. 4). Such findings led some public health experts to suggest that reducing
the carriage of serotypes associated with
antibiotic resistance by use of pneumococcal conjugate vaccine may have a greater
short-term impact than would decreasing
antibiotic use because decreasing antibiotic
use will take a long time before being widely
accepted.
In another specific case, the prevalence of
glycopeptide-resistant enterococci colonizing residents from Germany decreased
markedly following a progressive reduction
of the agricultural use of avoparcin (also a
glycopeptide antibiotic) throughout Western Europe (Fig. 5), according to Ingo Klare
and colleagues at the Robert Koch Institute
in Germany. Here again, there was some
delay after antibiotic use was reduced before resistance carriage rates came down.
The role of exchanges of resistance genes
among bacteria within the commensal
flora as such ecosystems adapt to new environmental conditions remains to be investigated.
It seems also that differences exist between
antibiotic regimens in terms of selection of resistant bacteria in the commensal flora, but data
are sparse. Indeed, we showed in my laboratory
that when antibiotics from different classes—for
instance, amoxiclav versus ofloxacin or telithromycin—are compared, strains resistant to the
antibiotic absorbed by particular patients are
preferentially selected. Moreover, among newborn patients in intensive care units, usage of
penicillin-tobramycin instead of ampicillin-cefotaxime as first-line empiric treatment is associated with dramatic reductions in colonization
of such newborns by drug-resistant gram-negative rods, according to Peter de Man and colleagues from Erasmus University in the Netherlands. Furthermore, there was also a borderline
trend towards reducing secondary infection rates.
Altogether, it appears that the need to curb
antibiotic resistance will have to take into account the role of the commensal flora in the
development of resistance. This may result in
profound changes, certainly quantitative but
also qualitative, in the ways we currently use
antibiotics.
SUGGESTED READING
Chen, D., A. McGeer, J. De Azavedo, and D. Low. 1999. Decreased susceptibility of Streptococcus pneumoniae to
fluoroquinolones in Canada. N. Engl. J. Med. 341:233–239.
de Man, P., B. A. Verhoeven, H. A. Verbrugh, M. C. Vos, and J. N. van den Anker. 2000. An antibiotic policy to prevent
emergence of resistant bacilli. Lancet 355:973–978.
Donskey, C. J., T. K. Chowdhry, M. T. Hecker, C. K. Hoyen, J. A. Hanrahan, A. M. Hujer, R. A. Hutton-Thomas, C. C.
Whalen, R. A. Bonomo, and L. B. Rice. 2000. Effect of antibiotic therapy on the density of vancomycin-resistant enterococci
in the stool of colonized patients. N. Engl. J. Med. 343:1925–1932.
Duval-Iflah, Y., P. Raibaud, C. Tancrede, and M. Rousseau. 1980. R-plasmid transfer from Serratia liquefaciens to
Escherichia coli in vitro and in vivo in the digestive tract of gnotobiotic mice associated with human fecal flora. Infect Immun
28:981–990.
Klare, I., D. Badstubner, C. Konstabel, G. Bohme, H. Claus, and W. Witte. 1999. Decreased incidence of VanA-type
vancomycin-resistant enterococci isolated from poultry meat and from fecal samples of humans in the community after
discontinuation of avoparcin usage in animal husbandry. Microb. Drug Resist. 5:45–52.
Martin, J. N., D. A. Rose, W. K. Hadley, F. Perdreau-Remington, P. K. Lam, and J. L. Gerberding. 1999. Emergence of
trimethoprim-sulfamethoxazole resistance in the AIDS era. J. Infect. Dis. 180:1809 –1818.
McCartney, A. L., W. Wenzhi, and G. W. Tannock. 1996. Molecular analysis of the composition of the bifidobacterial and
lactobacillus microflora of humans. Appl. Environ. Microbiol. 62:4608 – 4613.
Murray, B. E., E. R. Rensimer, and H. L. DuPont. 1982. Emergence of high-level trimethoprim resistance in fecal Escherichia
coli during oral administration of trimethoprim or trimethoprim-sulfamethoxazole. N. Engl. J. Med. 306:130 –135.
Walson, J. L., B. Marshall, B. M. Pokhrel, K. K. Kafle, and S. B. Levy. 2001. Carriage of antibiotic-resistant fecal bacteria in
Nepal reflects proximity to Kathmandu. J Infect. Dis. 184:1163–9.
Wu, S. W., H. de Lencastre, and A. Tomasz. 2001. Recruitment of the mecA gene homologue of Staphylococcus sciuri into a
resistance determinant and expression of the resistant phenotype in Staphylococcus aureus. J. Bacteriol. 183:2417–2424.
Volume 69, Number 12, 2003 / ASM News Y 607